[2023-03-17 06:30:51,150] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:51,150] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:51,150] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4a7b2c5-d76a-4de6-874e-178178798d26/dqc_reference
[2023-03-17 06:30:52,247] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:52,248] [INFO] Task started: Prodigal
[2023-03-17 06:30:52,248] [INFO] Running command: cat /var/lib/cwl/stg65a0f7ba-933f-4e90-9c64-378820939e81/OceanDNA-b9757.fa | prodigal -d OceanDNA-b9757/cds.fna -a OceanDNA-b9757/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:09,014] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:09,015] [INFO] Task started: HMMsearch
[2023-03-17 06:31:09,015] [INFO] Running command: hmmsearch --tblout OceanDNA-b9757/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4a7b2c5-d76a-4de6-874e-178178798d26/dqc_reference/reference_markers.hmm OceanDNA-b9757/protein.faa > /dev/null
[2023-03-17 06:31:09,195] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:09,196] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg65a0f7ba-933f-4e90-9c64-378820939e81/OceanDNA-b9757.fa]
[2023-03-17 06:31:09,216] [INFO] Query marker FASTA was written to OceanDNA-b9757/markers.fasta
[2023-03-17 06:31:09,217] [INFO] Task started: Blastn
[2023-03-17 06:31:09,217] [INFO] Running command: blastn -query OceanDNA-b9757/markers.fasta -db /var/lib/cwl/stgd4a7b2c5-d76a-4de6-874e-178178798d26/dqc_reference/reference_markers.fasta -out OceanDNA-b9757/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:09,688] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:09,689] [INFO] Selected 16 target genomes.
[2023-03-17 06:31:09,689] [INFO] Target genome list was writen to OceanDNA-b9757/target_genomes.txt
[2023-03-17 06:31:09,697] [INFO] Task started: fastANI
[2023-03-17 06:31:09,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a0f7ba-933f-4e90-9c64-378820939e81/OceanDNA-b9757.fa --refList OceanDNA-b9757/target_genomes.txt --output OceanDNA-b9757/fastani_result.tsv --threads 1
[2023-03-17 06:31:18,881] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:18,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4a7b2c5-d76a-4de6-874e-178178798d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:18,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4a7b2c5-d76a-4de6-874e-178178798d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:18,890] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:18,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:18,890] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	94.9434	348	389	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	79.3299	214	389	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	79.3299	214	389	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	79.1736	222	389	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	79.1736	222	389	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	78.9387	174	389	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	78.887	176	389	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	78.5909	176	389	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	78.3209	183	389	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	78.0202	174	389	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	77.9984	174	389	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	77.8832	139	389	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	77.8092	138	389	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.8652	86	389	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:18,890] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9757/tc_result.tsv
[2023-03-17 06:31:18,890] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:18,890] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:18,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4a7b2c5-d76a-4de6-874e-178178798d26/dqc_reference/checkm_data
[2023-03-17 06:31:18,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:18,895] [INFO] Task started: CheckM
[2023-03-17 06:31:18,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9757/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9757/checkm_input OceanDNA-b9757/checkm_result
[2023-03-17 06:32:04,940] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:04,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:04,951] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:04,952] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:04,952] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9757/markers.fasta)
[2023-03-17 06:32:04,952] [INFO] Task started: Blastn
[2023-03-17 06:32:04,952] [INFO] Running command: blastn -query OceanDNA-b9757/markers.fasta -db /var/lib/cwl/stgd4a7b2c5-d76a-4de6-874e-178178798d26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9757/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:05,480] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:05,481] [INFO] Selected 17 target genomes.
[2023-03-17 06:32:05,481] [INFO] Target genome list was writen to OceanDNA-b9757/target_genomes_gtdb.txt
[2023-03-17 06:32:05,610] [INFO] Task started: fastANI
[2023-03-17 06:32:05,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a0f7ba-933f-4e90-9c64-378820939e81/OceanDNA-b9757.fa --refList OceanDNA-b9757/target_genomes_gtdb.txt --output OceanDNA-b9757/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:16,393] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:16,403] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:16,403] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003992615.1	s__Muricauda beolgyonensis	94.9434	348	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584165.1	s__Muricauda sp003584165	79.3299	214	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584135.1	s__Muricauda sp003584135	79.1736	222	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003584105.1	s__Muricauda taeanensis	78.887	176	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_003058265.1	s__Muricauda sp003058265	78.5909	176	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	78.4692	166	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	78.3209	183	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCA_002699205.1	s__Muricauda sp002699205	78.1587	141	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
GCF_001683915.1	s__Muricauda sp001683915	78.1478	144	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_900102925.1	s__Muricauda zhangzhouensis	78.0202	174	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013407935.1	s__Muricauda sp013407935	78.0051	168	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.58	96.50	0.87	0.86	8	-
GCF_009184425.1	s__Muricauda olearia	77.8832	139	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_003385855.1	s__Muricauda sp003385855	77.8101	157	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_004916895.1	s__Muricauda alvinocaridis	77.787	139	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	76.8652	86	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.6119	70	389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:16,403] [INFO] GTDB search result was written to OceanDNA-b9757/result_gtdb.tsv
[2023-03-17 06:32:16,403] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:16,405] [INFO] DFAST_QC result json was written to OceanDNA-b9757/dqc_result.json
[2023-03-17 06:32:16,405] [INFO] DFAST_QC completed!
[2023-03-17 06:32:16,405] [INFO] Total running time: 0h1m25s